.TH g_polystat 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_polystat - calculates static properties of polymers

.B VERSION 4.5
.SH SYNOPSIS
\f3g_polystat\fP
.BI "\-s" " topol.tpr "
.BI "\-f" " traj.xtc "
.BI "\-n" " index.ndx "
.BI "\-o" " polystat.xvg "
.BI "\-v" " polyvec.xvg "
.BI "\-p" " persist.xvg "
.BI "\-i" " intdist.xvg "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-tu" " enum "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-[no]mw" ""
.BI "\-[no]pc" ""
.SH DESCRIPTION
\&g_polystat plots static properties of polymers as a function of time
\&and prints the average.


\&By default it determines the average end\-to\-end distance and radii
\&of gyration of polymers. It asks for an index group and split this
\&into molecules. The end\-to\-end distance is then determined using
\&the first and the last atom in the index group for each molecules.
\&For the radius of gyration the total and the three principal components
\&for the average gyration tensor are written.
\&With option \fB \-v\fR the eigenvectors are written.
\&With option \fB \-pc\fR also the average eigenvalues of the individual
\&gyration tensors are written.
\&With option \fB \-i\fR the mean square internal distances are
\&written.


\&With option \fB \-p\fR the persistence length is determined.
\&The chosen index group should consist of atoms that are
\&consecutively bonded in the polymer mainchains.
\&The persistence length is then determined from the cosine of
\&the angles between bonds with an index difference that is even,
\&the odd pairs are not used, because straight polymer backbones
\&are usually all trans and therefore only every second bond aligns.
\&The persistence length is defined as number of bonds where
\&the average cos reaches a value of 1/e. This point is determined
\&by a linear interpolation of log(cos).
.SH FILES
.BI "\-s" " topol.tpr" 
.B Input
 Run input file: tpr tpb tpa 

.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " index.ndx" 
.B Input, Opt.
 Index file 

.BI "\-o" " polystat.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-v" " polyvec.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-p" " persist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-i" " intdist.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-tu"  " enum" " ps" 
 Time unit: \fB fs\fR, \fB ps\fR, \fB ns\fR, \fB us\fR, \fB ms\fR or \fB s\fR

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-[no]mw"  "yes   "
 Use the mass weighting for radii of gyration

.BI "\-[no]pc"  "no    "
 Plot average eigenvalues

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
